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Saturday, December 03, 2005

About JChemPaint's future and todays 2.1.5 release

Stefan has done an excellent debugging week on JChemPaint, while I have been late with a 2.1 release. Anyway, I've just uploaded a Java 1.4 compiled JChemPaint 2.1 series release. I was told the (reported) bug count is down to one, so I expect to see the next stable branch to be released soon (2.2 series).

But what after JChemPaint 2.2 gets released? Will a 2.3 developers branch be opened? Or will the JChemPaint application, as we know it, cease to exist, and make place for the BioclipseJChemPaint plugin, that is being worked on?

It is worth mentioning the pros and cons of JChemPaint. One big pro is the applet version of JChemPaint, though free but closed source alternatives are available (e.g. MarvinSketch). Another advantage is the great semantics of the chemistry being drawn. For example, when drawing reactions, reactants are really marked as reactants, and are not just molecules left of an arrow. Moreover, JChemPaint is a great platform in which ideas can be tested! One of the key virtues of opensourceness. Cons include the limited amount of templates, print quality graphics, and others. (Comments on JChemPaint most welcomed.)

So what about this Bioclipse then? It is inheritently SWT based, but currently the SWT_AWT bridge is used to embed to current JChemPaint and underlying CDK code as is. Unfortunately, this bridge is using proprietary code from Sun (sun.awt classes), which makes it impossible to use with free virtual machines.

But there is also the option of using the SWT drawing classes. This has the advantage that it can be run with free virtual machines, and that it can even be compiled to native code. It requires serious rewriting of code in the JChemPaint and CDK code base. But, CDK's Renderer2D needs a rewrite anyway: it does not even use Swing's Java2D efficiently (try to figure out how it transforms atomic 2D coordinates into screen coordinates!). Some efforts have been ongoing, but a rewrite from scratch, with a better, more modular, design cannot hurd at all.

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

About Me

Assistant professor at the Dept of Bioinformatics - BiGCaT at NUTRIM, Maastricht University, studying biology at an unsupervised and atomic level. Open Science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and WikiPathways. ORCID:0000-0001-7542-0286. Posts on G+ are personal.

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